Is DST p.Glu1384fs (c.4152del) pathogenic?

DST p.Glu1384fs (c.4152del) is classified Pathogenic in DST (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-22). Absent from gnomAD; Associated with hereditary sensory and autonomic neuropathy type 6.

What condition is associated with DST p.Glu1384fs (c.4152del)?

DST p.Glu1384fs (c.4152del) is associated with hereditary sensory and autonomic neuropathy type 6, epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency (ClinVar).

How common is DST p.Glu1384fs (c.4152del) in the general population?

DST p.Glu1384fs (c.4152del) is absent from gnomAD (gnomAD).

DST p.Glu1384fs

Q: How is Hereditary sensory and autonomic neuropathy type 6 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.4152del · rs1247419225 · VCV1932718

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary sensory and autonomic neuropathy type 6

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 10	GERP 1.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DST
Protein: p.Glu1384fs
Coding: c.4152del
MANE Select: NM_001374736 · reported on NM_001723
dbSNP: rs1247419225
Type: Deletion
Location: chr6:56619882 (GRCh38)
Gene constraint: LOEUF 0.297 · pLI 1.00 (gnomAD)

Full DST gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary sensory and autonomic neuropathy type 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency

For Hereditary sensory and autonomic neuropathy type 6 (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

DST p.Glu1384Gln Uncertain significance ★ same residue
DST p.Thr1384Ala Uncertain significance ★ same residue
DST p.Ala1128fs Pathogenic ★★ same condition
DST p.Ala7253fs Pathogenic ★★ same condition
DST p.Arg4211_Lys4215del Uncertain significance ★★ same condition
DST p.Ser2388fs Uncertain significance ★★ same condition
DST c.14441-7del Benign/Likely benign ★★ same condition
DST c.21676-15_21676-14del Benign/Likely benign ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dst-p-glu1384fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown